Summary Transposable elements (TEs) are now recognized not only as parasitic DNA, whose spread in the genome must be controlled by the host, but also as major players in genome evolution and regulation1,2,3,4,5,6. Long INterspersed Element-1 (LINE-1 or L1), the only currently autonomous mobile transposon in humans, occupies 17% of the genome and continues to generate inter- and intra-individual genetic variation, in some cases resulting in disease1,2,3,4,5,6,7. Nonetheless, how L1 activity is controlled and what function L1s play in host gene regulation remain incompletely understood. Here, we use CRISPR/Cas9 screening strategies in two distinct human cell lines to provide the first genome-wide survey of genes involved in L1 retrotransposition control. We identified functionally diverse genes that either promote or restrict L1 retrotransposition. These genes, often associated with human diseases, control the L1 lifecycle at transcriptional or post-transcriptional levels and in a manner that can depend on the endogenous L1 sequence, underscoring the complexity of L1 regulation. We further investigated L1 restriction by MORC2 and human silencing hub (HUSH) complex subunits MPP8 and TASOR8. HUSH/MORC2 selectively bind evolutionarily young, full-length L1s located within transcriptionally permissive euchromatic environment, and promote H3K9me3 deposition for transcriptional silencing. Interestingly, these silencing events often occur within introns of transcriptionally active genes and lead to down-regulation of host gene expression in a HUSH/MORC2-dependent manner. Together, we provide a rich resource for studies of L1 retrotransposition, elucidate a novel L1 restriction pathway, and illustrate how epigenetic silencing of TEs rewires host gene expression programs.

Engineering and study of protein function by directed evolution has been limited by the requirement to introduce DNA libraries of defined size or to use global mutagenesis. Here, we develop a strategy to repurpose the somatic hypermutation machinery used in antibody affinity maturation to efficiently perform protein engineering in situ. Using catalytically inactive Cas9 (dCas9) to recruit variants of the deaminase AID (CRISPR-X), we can specifically mutagenize endogenous targets with limited off-target damage. This generates diverse libraries of localized point mutations, in contrast to insertions and deletions created by active Cas9, and can be used to mutagenize multiple genomic locations simultaneously. With this technology, we mutagenize GFP and select for spectrum-shifted variants, including EGFP. In addition, we mutate the target of the cancer therapeutic bortezomib, PSMB5, and identify known and novel mutations that confer resistance to treatment. Finally, we utilize a hyperactive AID variant with dramatically increased activity to mutagenize endogenous loci both upstream and downstream of transcriptional start sites. These experiments illustrate a powerful new approach to create highly complex libraries of genetic variants in native context, which can be broadly applied to investigate and improve protein function.

A fraction of ribosomes engaged in translation will fail to terminate when reaching a stop codon, yielding nascent proteins inappropriately extended on their C-termini. Although such extended proteins can interfere with normal cellular processes, known mechanisms of translational surveillance are insufficient to protect cells from potential dominant consequences. Through a combination of transgenics and CRISPR/Cas9 gene editing in C. elegans, we demonstrate a consistent ability of cells to block accumulation of C-terminal extended proteins that result from failure to terminate at stop codons. 3’UTR-encoded sequences were sufficient to lower protein levels. Measurements of mRNA levels and translation suggested a co- or post-translational mechanism of action for these sequences in C. elegans. Similar mechanisms evidently operate in human cells, where we observed a comparable tendency for translated human 3’UTR sequences to reduce mature protein expression in tissue culture assays, including 3' sequences from the hypomorphic “Constant Spring” hemoglobin stop codon variant. We suggest 3’UTRs may encode peptide sequences that destabilize the attached protein, providing mitigation of unwelcome and varied translation errors.

Efficient mRNA splicing is a prerequisite for protein biosynthesis and the eukaryotic splicing machinery is evolutionarily conserved among species of various phyla. At its catalytic core resides the activated splicing complex Bact consisting of the three small nuclear ribonucleoprotein complexes (snRNPs) U2, U5 and U6 and the so-called NineTeen complex (NTC) which is important for spliceosomal activation. CWC15 is an integral part of the NTC in humans and it is associated with the NTC in other species. Here we show the ubiquitous expression and developmental importance of the Arabidopsis ortholog of yeast CWC15. CWC15 associates with core components of the Arabidopsis NTC and its loss leads to inefficient splicing. Consistent with the central role of CWC15 in RNA splicing, cwc15 mutants are embryo lethal and additionally display strong defects in the female haploid phase. Interestingly, the haploid male gametophyte or pollen in Arabidopsis, on the other hand, can cope without functional CWC15, suggesting that developing pollen might be more tolerant to CWC15-mediated defects in splicing than either embryo or female gametophyte. Angiosperms are the predominant group of land plants. A hallmark of this dominance in the course of evolution is the establishment of a reduced haploid phase (called gametophyte) in the life cycle of flowering plants. In free-living gametophytes of mosses, the gametophytic generation forms independently recognizable plants that can even be the dominant structure. In contrast, the gametophyte of flowering plants is reduced to a small dependent structure with an almost minimal number of cells and a short lifetime 1. In Arabidopsis, the female gametophyte is deeply embedded in sporophytic tissue, whereas the male gametophyte or pollen has to be released from the sporophytic anther tissue for pollination to occur. Upon successful pollen-stigma interaction, the pollen tube grows inside the transmitting tract towards the ovule. Recent research has revealed that several signaling molecules including peptides play a role in the guidance of the pollen tube, attraction by the female gametophyte and burst of the pollen tube tip within one of the two synergid cells. If any of the aforementioned processes is disrupted, fertilization does not take place. Several mutants with disruptions in these processes have been isolated in the past 1-3. Upon successful fertilization, the Arabidopsis zygote initiates a precise developmental program, which results in a heart-shaped embryo already comprising all major seedling organs: two primary leaves or cotyledons, a shoot meristem, a hypocotyl, and a primary root with a root meristem 4. This invariant embryo patterning and development is impaired in mutants defective for various cellular response pathways e.g. responses to phytohormones, small RNA pathways, vesicular trafficking, cytoskeletal structure, and cell cycle control 5-9. Furthermore, mutations in genes that are components of the RNA splicing machinery (spliceosome) affect gametophyte function and embryoge...